I am planning to analyze my 16S RNA sequences using Galaxy mothur Toolset.
I watched your youtube Tutorial GTN Training - Microbial Analysis - 16S Metagenomics and analyzed some test samples following the
But the problem is that my PCR amplification targeted the V3V4 region of the 16s rRNA, using the primers set 341F and 806R.
Can I still use the silvav4fasta database for alignment? Does it cover this region?
I tried downloading the latest version of silva 138.1 but there is an error and I cannot perform the align.seqs command.
I tried changing in silvav4 the start and end in the screen.seqs command but it didn’t work as well.
Could anyone please advise regarding this matter?